Competitiveness and communication for effective inoculation byRhizobium, Bradyrhizobium and vesicular-arbuscular mycorrhiza fungi

After a short summary on the ecology and rhizosphere biology of symbiotic bacteria and vesicular-arbuscular (VA) mycorrhiza fungi and their application as microbial inocula, results on competitiveness and communication are summarized. Stress factors such as high temperature, low soil pH, aluminium concentrations and phytoalexins produced by the host plants were studied withRhizobium leguminosarum bv.phaseoli andRhizobium tropici onPhaseolus beans. Quantitative data for competitiveness were obtained by usinggus + (glucoronidase) labelled strains, which produce blue-coloured nodules. ForPhaseolus-nodulating rhizobia, a group specific DNA probe was also developed, which did not hybridize with more than 20 other common soil and rhizosphere bacteria. Results from several laboratories contributing to knowledge of signal exchange and communication in theRhizobium/Bradyrhizobium legume system are summarized in a new scheme, including also defense reactions at the early stages of legume nodule initiation. Stimulating effects of flavonoids on germination and growth of VA mycorrhiza fungi were also found. A constitutive antifungal compound in pea roots, -isoxazolinonyl-alanine, was characterized

Draft Genome Sequence of Propionisporasp. Strain 2/2-37, a New Xylan-Degrading Bacterium Isolated from a Mesophilic Biogas Reactor

Koeck DE, Maus I, Wibberg D, et al. Draft Genome Sequence of Propionisporasp. Strain 2/2-37, a New Xylan-Degrading Bacterium Isolated from a Mesophilic Biogas Reactor. Genome Announcements. 2016;4(3):e00609-16.The novel mesophilic bacterial strain Propionispora sp. 2/2-37 was isolated from an industrial-scale biogas plant. Comparative 16S rRNA gene sequencing revealed that the isolate constitutes a new subcluster within the order Selenomonadales. The 2/2-37 draft genome sequence was established and provides the genetic basis for application of this microorganism in degradation of biomass for bio-fuel production

Complete Genome Sequence of Herbinix luporumSD1D, a New Cellulose-Degrading Bacterium Isolated from a Thermophilic Biogas Reactor

Koeck DE, Maus I, Wibberg D, et al. Complete Genome Sequence of Herbinix luporumSD1D, a New Cellulose-Degrading Bacterium Isolated from a Thermophilic Biogas Reactor. Genome Announcements. 2016;4(4):e00687-16.A novel cellulolytic bacterial strain was isolated from an industrial-scale biogas plant. The 16S rRNA gene sequence of the strain SD1D showed 96.4% similarity to Herbinix hemicellulosilytica T3/55T, indicating a novel species within the genus Herbinix (family Lachnospiraceae). Here, the complete genome sequence of Herbinix luporum SD1D is reported

Characterisation of symbiotically efficient alfalfa-nodulating rhizobia isolated from acid soils of Argentina and Uruguay

The diversity, growth and symbiotic behaviour of symbiotically efficient alfalfa-nodulating rhizobia isolated from acid soils of Argentina and Uruguay were analysed. Partial sequencing of the 16S rDNA indicated that these isolates belong to Sinorhizobium meliloti species. IS-fingerprinting analysis revealed a high diversity among the isolates but some of them appear related to inoculant strains currently used in the region. The S. meliloti isolates showed a decreased growth rate with increasing acidity. They were, however, able to nodulate alfalfa at pH 5.6, but showed a delayed nodulation and decreased nodule number typical of S. meliloti strains. The impaired nodulation of S. meliloti at pH 5.6 did not result in a reduction of alfalfa dry matter production or nitrogen content. However, significant differences were observed for the relative symbiotic effectiveness of the strains analysed. LPU63 (Argentina) was the most effective among the isolates and exhibited a high nodulation competitiveness at both neutral and acidic pH. These results suggest that the isolate LPU63 may be a potential efficient inoculant for alfalfa in acid soils.Instituto de Biotecnología y Biología Molecula

Unraveling the microbiome of a thermophilic biogas plant by metagenome and metatranscriptome analysis complemented by characterization of bacterial and archaeal isolates

One of the most promising technologies to sustainably produce energy and to mitigate greenhouse gas emissions from combustion of fossil energy carriers is the anaerobic digestion and biomethanation of organic raw material and waste towards biogas by highly diverse microbial consortia. In this context, the microbial systems ecology of thermophilic industrial-scale biogas plants is poorly understood

Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes

Background: To elucidate biogas microbial communities and processes, the application of high-throughput DNA analysis approaches is becoming increasingly important. Unfortunately, generated data can only partialy be interpreted rudimentary since databases lack reference sequences. Results: Novel cellulolytic, hydrolytic, and acidogenic/acetogenic Bacteria as well as methanogenic Archaea originating from different anaerobic digestion communities were analyzed on the genomic level to assess their role in biomass decomposition and biogas production. Some of the analyzed bacterial strains were recently described as new species and even genera, namely Herbinix hemicellulosilytica T3/55T, Herbinix luporum SD1DT, Clostridium bornimense M2/40T, Proteiniphilum saccharofermentans M3/6T, Fermentimonas caenicola ING2-E5BT, and Petrimonas mucosa ING2-E5AT. High-throughput genome sequencing of 22 anaerobic digestion isolates enabled functional genome interpretation, metabolic reconstruction, and prediction of microbial traits regarding their abilities to utilize complex bio-polymers and to perform specific fermentation pathways. To determine the prevalence of the isolates included in this study in different biogas systems, corresponding metagenome fragment mappings were done. Methanoculleus bourgensis was found to be abundant in three mesophilic biogas plants studied and slightly less abundant in a thermophilic biogas plant, whereas Defluviitoga tunisiensis was only prominent in the thermophilic system. Moreover, several of the analyzed species were clearly detectable in the mesophilic biogas plants, but appeared to be only moderately abundant. Among the species for which genome sequence information was publicly available prior to this study, only the species Amphibacillus xylanus, Clostridium clariflavum, and Lactobacillus acidophilus are of importance for the biogas microbiomes analyzed, but did not reach the level of abundance as determined for M. bourgensis and D. tunisiensis. Conclusions: Isolation of key anaerobic digestion microorganisms and their functional interpretation was achieved by application of elaborated cultivation techniques and subsequent genome analyses. New isolates and their genome information extend the repository covering anaerobic digestion community members. © 2017 The Author(s)

The missing link: Bordetella petrii is endowed with both the metabolic versatility of environmental bacteria and virulence traits of pathogenic Bordetellae

Gross R, Guzman CA, Sebaihia M, et al. The missing link: Bordetella petrii is endowed with both the metabolic versatility of environmental bacteria and virulence traits of pathogenic Bordetellae. BMC Genomics. 2008;9(1): 449.Background: Bordetella petrii is the only environmental species hitherto found among the otherwise host-restricted and pathogenic members of the genus Bordetella. Phylogenetically, it connects the pathogenic Bordetellae and environmental bacteria of the genera Achromobacter and Alcaligenes, which are opportunistic pathogens. B. petrii strains have been isolated from very different environmental niches, including river sediment, polluted soil, marine sponges and a grass root. Recently, clinical isolates associated with bone degenerative disease or cystic fibrosis have also been described. Results: In this manuscript we present the results of the analysis of the completely annotated genome sequence of the B. petrii strain DSMZ12804. B. petrii has a mosaic genome of 5,287,950 bp harboring numerous mobile genetic elements, including seven large genomic islands. Four of them are highly related to the clc element of Pseudomonas knackmussii B13, which encodes genes involved in the degradation of aromatics. Though being an environmental isolate, the sequenced B. petrii strain also encodes proteins related to virulence factors of the pathogenic Bordetellae, including the filamentous hemagglutinin, which is a major colonization factor of B. pertussis, and the master virulence regulator BvgAS. However, it lacks all known toxins of the pathogenic Bordetellae. Conclusion: The genomic analysis suggests that B. petrii represents an evolutionary link between free-living environmental bacteria and the host-restricted obligate pathogenic Bordetellae. Its remarkable metabolic versatility may enable B. petrii to thrive in very different ecological niches

EDGAR: A software framework for the comparative analysis of prokaryotic genomes

Blom J, Albaum S, Doppmeier D, et al. EDGAR: a software framework for the comparative analysis of prokaryotic genomes. BMC Bioinformatics. 2009;10(1): 154.Background:The introduction of next generation sequencing approaches has caused a rapid increase in the number of completely sequenced genomes. As one result of this development, it is now feasible to analyze large groups of related genomes in a comparative approach. A main task in comparative genomics is the identification of orthologous genes in different genomes and the classification of genes as core genes or singletons. Results: To support these studies EDGAR – ''Efficient Database framework for comparative Genome Analyses using BLAST score Ratios'' – was developed. EDGAR is designed to automatically perform genome comparisons in a high throughput approach. Comparative analyses for 582 genomes across 75 genus groups taken from the NCBI genomes database were conducted with the software and the results were integrated into an underlying database. To demonstrate a specific application case, we analyzed ten genomes of the bacterial genus Xanthomonas, for which phylogenetic studies were awkward due to divergent taxonomic systems. The resultant phylogeny EDGAR provided was consistent with outcomes from traditional approaches performed recently and moreover, it was possible to root each strain with unprecedented accuracy. Conclusion: EDGAR provides novel analysis features and significantly simplifies the comparative analysis of related genomes. The software supports a quick survey of evolutionary relationships and simplifies the process of obtaining new biological insights into the differential gene content of kindred genomes. Visualization features, like synteny plots or Venn diagrams, are offered to the scientific community through a web-based and therefore platform independent user interface http://edgar.cebitec.uni-bielefeld.de webcite, where the precomputed data sets can be browsed

Comparative and Joint Analysis of Two Metagenomic Datasets from a Biogas Fermenter Obtained by 454-Pyrosequencing

Biogas production from renewable resources is attracting increased attention as an alternative energy source due to the limited availability of traditional fossil fuels. Many countries are promoting the use of alternative energy sources for sustainable energy production. In this study, a metagenome from a production-scale biogas fermenter was analysed employing Roche's GS FLX Titanium technology and compared to a previous dataset obtained from the same community DNA sample that was sequenced on the GS FLX platform. Taxonomic profiling based on 16S rRNA-specific sequences and an Environmental Gene Tag (EGT) analysis employing CARMA demonstrated that both approaches benefit from the longer read lengths obtained on the Titanium platform. Results confirmed Clostridia as the most prevalent taxonomic class, whereas species of the order Methanomicrobiales are dominant among methanogenic Archaea. However, the analyses also identified additional taxa that were missed by the previous study, including members of the genera Streptococcus, Acetivibrio, Garciella, Tissierella, and Gelria, which might also play a role in the fermentation process leading to the formation of methane. Taking advantage of the CARMA feature to correlate taxonomic information of sequences with their assigned functions, it appeared that Firmicutes, followed by Bacteroidetes and Proteobacteria, dominate within the functional context of polysaccharide degradation whereas Methanomicrobiales represent the most abundant taxonomic group responsible for methane production. Clostridia is the most important class involved in the reductive CoA pathway (Wood-Ljungdahl pathway) that is characteristic for acetogenesis. Based on binning of 16S rRNA-specific sequences allocated to the dominant genus Methanoculleus, it could be shown that this genus is represented by several different species. Phylogenetic analysis of these sequences placed them in close proximity to the hydrogenotrophic methanogen Methanoculleus bourgensis. While rarefaction analyses still indicate incomplete coverage, examination of the GS FLX Titanium dataset resulted in the identification of additional genera and functional elements, providing a far more complete coverage of the community involved in anaerobic fermentative pathways leading to methane formation

Cloning of a Phosphinothricin N-Acetyltransferase Gene from Streptomyces-Viridochromogenes TU494 and its Expression in Streptomyces-Lividans and Escherichia-Coli

Strrauch E, Wohlleben W, Pühler A. Cloning of a Phosphinothricin N-Acetyltransferase Gene from Streptomyces-Viridochromogenes TU494 and its Expression in Streptomyces-Lividans and Escherichia-Coli. Gene. 1988;63(1):65-74